One blastomere of the two cell stage sea urchin embryo (Lytechinus variegatus) was labeled with an intracellular fluorescent lineage tracing stain to determine, from the lineage of that blastomere, the orientation of the first cleavage furrow with regard to the axes of bilateral symmetry in the gastrula and pluteus larva. Two methods were used to mark the blastomere: In the first, the lipophilic carbocyanine dye DiIC16 was microinjected directly into the blastomere after first cleavage was completed. In the second, caged (nonfluorescent) fluorescein-dextran was microinjected into the single-celled zygote and uncaged (made fluorescent) in one of the blastomeres at the two-cell stage using two-photon excitation microscopy (TPEM). This is the first use of TPEM for embryonic lineage tracing. In both methods the dye proved to be nontoxic and fluorescence was confined to lineally related cells. The results from both methods were similar and showed that the first cleavage furrow was variable in its orientation. Results were similar using animals obtained from different geographic locations. These results differ from those of McCain and McClay (Development, 1994, 120, 395-404), who reported that the median orientation was invariant in this species. The differences between the two studies are discussed. We conclude that first cleavage does not specify nor is it predictive of the bilateral axes in this species. The technique of TPEM is proffered as a powerful new tool that will enable the marking and tracing of embryonic cell lineages with less injury and more precision than current methods.